Tottenham reported 13 cases of coronavirus among their players and staff on the eve of the match, leading to the game being called off as a result.
Antonio Conte's side tried consulting with the Premier League to have their game against Leicester City last Thursday moved so the Rennes fixture can be fulfilled but the request was declined.
Leicester themselves had an outbreak within their squad and their league game against Spurs was also rescheduled.
UEFA referred referred the case to their Control, Ethics and Disciplinary body, who have ruled in favour of the French side.
It means that Tottenham finish in third position behind Rennes and Vitesse Arnhem.
"Following several positive cases of COVID-19 that were identified from players and staff of Tottenham Hotspur FC, the UEFA Europa Conference League group stage match between Tottenham Hotspur FC and Stade Rennais FC -- scheduled to be played on Dec. 9,2021 in London, United Kingdom -- could not be played," a UEFA statement released on Monday read.
"The matter was submitted to the UEFA Control, Ethics and Disciplinary Body, for a decision to be taken in accordance with Annex J of the Regulations of the UEFA Europa Conference League (2021-22 Season).
"Based on the Article 30 (4) of the UEFA Disciplinary Regulations and given the urgent circumstances of the matter, the ad-hoc chairman of the Control, Ethics and Disciplinary Body referred the case to the Appeals Body.
"The Chairman of the UEFA Appeals Body took the following decision: to declare the UEFA Europa Conference League group stage match between Tottenham Hotspur FC and Stade Rennais FC, that was initially scheduled to be played on 9 December 2021, as forfeited by Tottenham Hotspur FC, who is therefore deemed to have lost the match 0-3."
Tottenham Hotspurs have since returned to action, holding Liverpool to a 2-2 draw in the Premier League on Sunday.
